Reappraisal of immunohistochemical profiling of special histological types of breast carcinomas: a study of 121 cases of eight different subtypes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

High resolution ultra high pressure liquid chromatography-time-of-flight mass spectrometry dereplication strategy for the metabolite profiling of Brazilian Lippia species

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Galectin-3 Overexpression in Invasive Laryngeal Carcinoma, Assessed by Computer-assisted Analysis

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Conditional reasoning: A key to assessing computer-based knowledge-building communication processes

This article describes a methodological approach to conditional reasoning in online asynchronous learning environments such as Virtual-U VGroups, developed by SFU, BC, Canada, consistent with the notion of meaning implication: If part of a meaning C is embedded in B and a part of a meaning B is embedded in A, then A implies C in terms of meaning [Piaget 91]. A new transcript analysis technique was developed to assess the flows of conditional meaning implications and to identify the occurrence of hypotheses and connections among them in two human science graduate mixed-mode online courses offered in the summer/spring session of 1997 by SFU. Flows of conditional meaning implications were confronted with Virtual-U VGroups threads and results of the two courses were compared. Findings suggest that Virtual-U VGroups is a knowledge-building environment although the tree-like Virtual-U VGroups threads should be transformed into neuronal-like threads. Findings also suggest that formulating hypotheses together triggers a collaboratively problem-solving process that scaffolds knowledge-building in asynchronous learning environments: A pedagogical technique and an built-in tool for formulating hypotheses together are proposed. © Springer Pub. Co.

Study of water and dimethylformamide interaction by computer simulation

Monte Carlo simulations of water-dimethylformamide (DMF) mixtures were performed in the isothermal and isobaric ensemble at 298.15 K and 1 atm. The intermolecular interaction energy was calculated using the classical 6-12 Lennard-Jones pairwise potential plus a Coulomb term. The TIP4P model was used for simulating water molecules, and a six-site model previously optimised by us was used to represent DMF. The potential energy for the water-DMF interaction was obtained via standard geometric combining rules using the original potential parameters for the pure liquids. The radial distribution functions calculated for water-DMF mixtures show well characterised hydrogen bonds between the oxygen site of DMF and hydrogen of water. A structureless correlation curve was observed for the interaction between the hydrogen site of the carbonyl group and the oxygen site of water. Hydration effects on the stabilisation of the DMF molecule in aqueous solution have been investigated using statistical perturbation theory. The results show that energetic changes involved in the hydration process are not strong enough to stabilise another configuration of DMF than the planar one.

Turning math attractive to computer science students: an application-to-model approach

This paper describes an innovative approach to develop the understanding about the relevance of mathematics to computer science. The mathematical subjects are introduced through an application-to-model scheme that lead computer science students to a better understanding of why they have to learn math and learn it effectively. Our approach consists of a single one semester course, taught at the first semester of the program, where the students are initially exposed to some typical computer applications. When they recognize the applications' complexity, the instructor gives the mathematical models supporting such applications, even before a formal introduction to the model in a math course. We applied this approach at Unesp (Brazil) and the results include a large reduction in the rate of students that abandon the college and better students in the final years of our program.

A flexible curriculum for computer science undergraduate major

This paper describes an innovative approach to establish a CS curriculum, aiming flexibility and minimization of the time spent in the classrooms. This approach has been developed at the Paulista State University - Unesp - at São José do Rio Preto, and is producing very interesting results. The load reduction is achieved through a series of fundamental core and breadth courses that precede depth courses in specific areas. The flexibility comes as a side effect of the depth courses, which can be adapted without any changes in the core courses. In the following pages we fully describe our motivations, actions and results.

A computer-assisted approach for chemotaxonomic studies - Diterpenes in Lamiaceae

This paper describes a new computer approach for chemotaxonomic studies. The methodology employed enables the search for chemical substructures as taxonomic descriptors using all expert system built with plant natural products. The operation of the system was tested with diterpenes as taxonomic markers in Lamiaceae. © 2001 Elsevier Science Ltd.

An attack signature model to computer security intrusion detection

Internal and external computer network attacks or security threats occur according to standards and follow a set of subsequent steps, allowing to establish profiles or patterns. This well-known behavior is the basis of signature analysis intrusion detection systems. This work presents a new attack signature model to be applied on network-based intrusion detection systems engines. The AISF (ACME! Intrusion Signature Format) model is built upon XML technology and works on intrusion signatures handling and analysis, from storage to manipulation. Using this new model, the process of storing and analyzing information about intrusion signatures for further use by an IDS become a less difficult and standardized process.

Computer-assisted analysis of p53 and PCNA expression in oral lesions infected with human papillomavirus

OBJECTIVE: To carry out a retrospective study to determine whether human papillomavirus (HPV) infection and immunohistochemical expression of p53 and proliferating cell nuclear antigen (PCNA) are related to the risk of oral cancer. STUDY DESIGN: Fifty-seven oral biopsies, consisting of 30 oral squamous papillomas (OSPs) and 27 oral squamous cell carcinomas (OSCCs) were tested for the presence of HPV 6/11 and 16/18 by in situ hybridization using catalyzed signal amplification and in situ hybridization. p53 And PCNA expression was analyzed by immunohistochemistry and evaluated quantitatively by image analysis. RESULTS: Nineteen of the 57 oral lesions (33.3%) were positive for HPV. HPV 6/11 was found in 6 of 30 (20%) OSPs and 1 of 27 (3.7%) OSCCs. HPV 16/18 was found in 10 of 27 (37%) OSCCs and 2 of 30 (6.7%) OSPs. Sixteen of the 19 HPV-positive cases (84.2%) were p53 negative; 5 (9%) were HPV 6/11 and 11 (19%) HPV 16/18, with an inverse correlation between the presence of HPV DNA and p53 expression (P=.017, P < .05). PCNA expression appeared in 18 (94.7%) of HPV positive cases, showing that HPV 16/18 was associated with intensity of PCNA expression and with OSCCs (P=.037, P < .05). CONCLUSION: Quantitative evaluation of p53 by image analysis showed an inverse correlation between p53 expression and HPV presence, suggesting protein degradation. Image analysis also demonstrated that PCNA expression was more intense in HPV DNA 16/18 OSCCs. These findings suggest involvement of high-risk HPV types in oral carcinogenesis.

An environment for knowledge discovery in biology

This paper describes a data mining environment for knowledge discovery in bioinformatics applications. The system has a generic kernel that implements the mining functions to be applied to input primary databases, with a warehouse architecture, of biomedical information. Both supervised and unsupervised classification can be implemented within the kernel and applied to data extracted from the primary database, with the results being suitably stored in a complex object database for knowledge discovery. The kernel also includes a specific high-performance library that allows designing and applying the mining functions in parallel machines. The experimental results obtained by the application of the kernel functions are reported. © 2003 Elsevier Ltd. All rights reserved.

Two dimensional computer simulation of plasma immersion ion implantation

The biggest advantage of plasma immersion ion implantation (PIII) is the capability of treating objects with irregular geometry without complex manipulation of the target holder. The effectiveness of this approach relies on the uniformity of the incident ion dose. Unfortunately, perfect dose uniformity is usually difficult to achieve when treating samples of complex shape. The problems arise from the non-uniform plasma density and expansion of plasma sheath. A particle-in-cell computer simulation is used to study the time-dependent evolution of the plasma sheath surrounding two-dimensional objects during process of plasma immersion ion implantation. Before starting the implantation phase, steady-state nitrogen plasma is established inside the simulation volume by using ionization of gas precursor with primary electrons. The plasma self-consistently evolves to a non-uniform density distribution, which is used as initial density distribution for the implantation phase. As a result, we can obtain a more realistic description of the plasma sheath expansion and dynamics. Ion current density on the target, average impact energy, and trajectories of the implanted ions were calculated for three geometrical shapes. Large deviations from the uniform dose distribution have been observed for targets with irregular shapes. In addition, effect of secondary electron emission has been included in our simulation and no qualitative modifications to the sheath dynamics have been noticed. However, the energetic secondary electrons change drastically the plasma net balance and also pose significant X-ray hazard. Finally, an axial magnetic field has been added to the calculations and the possibility for magnetic insulation of secondary electrons has been proven.